Hi, Do you really need those restraints to maintain the integrity of the beta sheet at 3 ang. resolution? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Apr 27, 2021 19:04, Matthias Uthoff wrote: Hi phenixbb, I am working on a homodimer. Each protein has an internal b-sheet with three b-strands, however the sheets swap their middle strands. So a sheet consists of one strand from molecule A surrounded by two strands from molecule B or vice versa. As I am at 3 A resolution, I would like to set secondary structure restraints including correct hydrogen bonding between the strands of the two molecules. My problem: There is only one protein in the ASU and the "other" molecule is in deed just a symmetry mate. Phenix is not able to automatically detect this and if I provide the restraints myself, phenix discards them as it is falsely assuming the b-sheet is intramolecularly (all on chain A) and hence the strands are 30ish A apart. What is the best way of refining this feature? Thanks in advance, Matthias -- Matthias Uthoff, PhD Student University of Cologne Institute for Biochemistry Zülpicher Straße 47 D-50674 Cologne Phone: +49 221 470 3211 E-Mail:[email protected] Internet:http://px.uni-koeln.de _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Hi Matthias, You may try to specify H-bonds manually using custom bond restraints mechanism which supports bonds over symmetry: https://www.phenix-online.org/documentation/reference/refinement.html#defini... You will not get angle restraints around H-bonds in this case. I believe the most straight-forward approach would be to take Bruno's suggestion about expanding the molecule and apply NCS constraints to ensure the copies stay identical. Best regards, Oleg Sobolev. On Tue, Apr 27, 2021 at 9:04 AM Matthias Uthoff < [email protected]> wrote:

Hi phenixbb,

I am working on a homodimer. Each protein has an internal b-sheet with three b-strands, however the sheets swap their middle strands. So a sheet consists of one strand from molecule A surrounded by two strands from molecule B or vice versa. As I am at 3 A resolution, I would like to set secondary structure restraints including correct hydrogen bonding between the strands of the two molecules.

My problem: There is only one protein in the ASU and the "other" molecule is in deed just a symmetry mate.

Phenix is not able to automatically detect this and if I provide the restraints myself, phenix discards them as it is falsely assuming the b-sheet is intramolecularly (all on chain A) and hence the strands are 30ish A apart.

What is the best way of refining this feature?

Thanks in advance,

Matthias

-- Matthias Uthoff, PhD Student

University of Cologne Institute for Biochemistry Zülpicher Straße 47 D-50674 Cologne

Phone: +49 221 470 3211 E-Mail:[email protected] Internet:http://px.uni-koeln.de

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